Multivariate optimal allocation for different domains in one and two stages stratified sample design. R2BEAT extends the Neyman (1934) â Tschuprow (1923) allocation method to the case of several variables, adopting a generalization of the Bethelâ s proposal (1989). R2BEAT develops this methodology but, moreover, it allows to determine the sample allocation in the multivariate and multi-domains case of estimates for two-stage stratified samples. It also allows to perform both Primary Stage Units and Secondary Stage Units selection. This package requires the availability of ReGenesees', that can be installed from <https://github.com/DiegoZardetto/ReGenesees>.

Population genetic data such as Single Nucleotide Polymorphisms (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an Extended Haplotype Homozygosity (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: iHS (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or Darwinian selection within a single population as well as Rsb (Tang 2007) <doi:10.1371/journal.pbio.0050171> and XP-EHH (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.

This package implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.

Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates. For more details see Sterratt, D. C., Lyngholm, D., Willshaw, D. J. and Thompson, I. D. (2013) <doi:10.1371/journal.pcbi.1002921>.

This package provides the Jester Dataset for package recommenderlab.

This package provides a very lightweight package that writes out log messages in an opinionated way. Simpler and lighter than other logging packages, rlog provides a compact feature set that focuses on getting the job done in a Unix-like way.

Retrieve, map and summarize data from the VertNet.org archives (<https://vertnet.org/>). Functions allow searching by many parameters, including taxonomic names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large datasets via email.

This package provides functions from the book "Reinsurance: Actuarial and Statistical Aspects" (2017) by Hansjoerg Albrecher, Jan Beirlant and Jef Teugels <https://www.wiley.com/en-us/Reinsurance%3A+Actuarial+and+Statistical+Aspects-p-9780470772683>.

Extension to REddyProc that allows reading data from netCDF files.

Utility functions for interacting with the COMPADRE and COMADRE databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.

Makes easier the creation of R package or research compendium (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files. A full ready-to-work structure is set up with some additional features: version control, remote repository creation, CI/CD configuration (check package integrity under several OS, test code with testthat', and build and deploy website using pkgdown'). This package heavily relies on the R packages devtools and usethis and follows recommendations made by Wickham H. (2015) <ISBN:9781491910597> and Marwick B. et al. (2018) <doi:10.7287/peerj.preprints.3192v2>.

This package provides functions allowing the user to recursively extract frequent patterns and confident rules according to indicators of minimal support and minimal confidence. These functions are described in "Recursive Association Rule Mining" Abdelkader Mokkadem, Mariane Pelletier, Louis Raimbault (2020) <arXiv:2011.14195>.

Proper L2-penalized maximum likelihood estimators for precision matrices and supporting functions to employ these estimators in a graphical modeling setting. For details, see Peeters, Bilgrau, & van Wieringen (2022) <doi:10.18637/jss.v102.i04> and associated publications.

Streamlined statistical reporting in Rmarkdown environments. Facilitates the automated reporting of descriptive statistics, multiple univariate models, multivariable models and tables combining these outputs. Plotting functions include customisable survival curves, forest plots from logistic and ordinal regression and bivariate comparison plots.

An extremely simple stack data type, implemented with R6 classes. The size of the stack increases as needed, and the amortized time complexity is O(1). The stack may contain arbitrary objects.

Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.

R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.

Leaf angle distribution is described by a number of functions (e.g. ellipsoidal, Beta and rotated ellipsoidal). The parameters of leaf angle distributions functions are estimated through different empirical relationship. This package includes estimations of parameters of different leaf angle distribution function, plots and evaluates leaf angle distribution functions, calculates extinction coefficients given leaf angle distribution. Reference: Wang(2007)<doi:10.1016/j.agrformet.2006.12.003>.

Implementation of the MaxRank normalization method, which enables standardization of Rank Abundance Distributions (RADs) to a specified number of ranks. Rank abundance distributions are widely used in biology and ecology to describe species abundances, and are mathematically equivalent to complementary cumulative distribution functions (CCDFs) used in physics, linguistics, sociology, and other fields. The method is described in Saeedghalati et al. (2017) <doi:10.1371/journal.pcbi.1005362>.

Risk-related information (like the prevalence of conditions, the sensitivity and specificity of diagnostic tests, or the effectiveness of interventions or treatments) can be expressed in terms of frequencies or probabilities. By providing a toolbox of corresponding metrics and representations, riskyr computes, translates, and visualizes risk-related information in a variety of ways. Adopting multiple complementary perspectives provides insights into the interplay between key parameters and renders teaching and training programs on risk literacy more transparent (see <doi:10.3389/fpsyg.2020.567817>, for details).

Facilitates making a connection to the Revenera API and executing various queries. You can use it to get event data and metadata. The Revenera documentation is available at <https://rui-api.redoc.ly/>. This package is not supported by Flexera (owner of the software).

Implementation of a Principal Component Analysis (PCA) in the torus via density ridge estimation. The main function, ridge_pca(), obtains the relevant density ridge for bivariate sine von Mises and bivariate wrapped Cauchy distribution models and provides the associated scores and variance decomposition. Auxiliary functions for evaluating, fitting, and sampling these models are also provided. The package provides replicability to Garcà a-Portugués and Prieto-Tirado (2023) <doi:10.1007/s11222-023-10273-9>.

The LabKey client library for R makes it easy for R users to load live data from a LabKey Server, <https://www.labkey.com/>, into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a LabKey Server, provided they have appropriate permissions to do so.

This package implements efficient simulation procedures to estimate tail loss probabilities and conditional excess for a stock portfolio. The log-returns are assumed to follow a t-copula model with generalized hyperbolic or t marginals.